FMO DATABASE

FMODB ID: KGMR3

Calculation Name: 2X3D-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2X3D

Chain ID: A

ChEMBL ID:

UniProt ID: Q97ZR0

Base Structure: X-ray

Registration Date: 2023-09-23

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptHSide
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	90
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-591410.91043
FMO2-HF: Nuclear repulsion	555946.912894
FMO2-HF: Total energy	-35463.997537
FMO2-MP2: Total energy	-35563.688903

3D Structure Molmil

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:0:GLY)

Summations of interaction energy for fragment #1(A:0:GLY)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
-3.12	-0.513	-0.004	-1.408	-1.194	0.002

Interaction energy analysis for fragmet #1(A:0:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.019 / q_NPA : 0.007

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

Sort

Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	2	ALA	0	-0.002	0.005	3.738	-0.285	2.033	-0.013	-1.287	-1.018	0.003
4	A	3	ILE	0	0.044	0.027	5.835	0.342	0.342	0.000	0.000	0.000	0.000
5	A	4	ARG	1	0.803	0.906	7.081	1.446	1.446	0.000	0.000	0.000	0.000
6	A	5	ARG	1	0.776	0.843	10.684	0.404	0.404	0.000	0.000	0.000	0.000
7	A	6	LEU	0	-0.030	-0.007	14.289	0.030	0.030	0.000	0.000	0.000	0.000
8	A	7	VAL	0	0.022	0.012	16.882	-0.003	-0.003	0.000	0.000	0.000	0.000
9	A	8	LEU	0	-0.039	-0.027	19.630	0.017	0.017	0.000	0.000	0.000	0.000
10	A	9	ASP	-1	-0.797	-0.867	22.871	-0.145	-0.145	0.000	0.000	0.000	0.000
11	A	10	VAL	0	-0.036	-0.044	25.268	0.001	0.001	0.000	0.000	0.000	0.000
12	A	11	LEU	0	0.035	0.029	28.100	0.009	0.009	0.000	0.000	0.000	0.000
13	A	12	LYS	1	0.885	0.926	31.094	0.152	0.152	0.000	0.000	0.000	0.000
14	A	13	PRO	0	0.062	0.044	33.012	0.009	0.009	0.000	0.000	0.000	0.000
15	A	14	ILE	0	-0.049	-0.019	36.196	-0.008	-0.008	0.000	0.000	0.000	0.000
16	A	15	ARG	1	0.887	0.939	38.213	0.098	0.098	0.000	0.000	0.000	0.000
17	A	16	GLY	0	0.028	0.006	36.466	0.002	0.002	0.000	0.000	0.000	0.000
18	A	17	THR	0	-0.007	-0.016	30.582	0.008	0.008	0.000	0.000	0.000	0.000
19	A	18	SER	0	-0.064	-0.042	33.485	-0.001	-0.001	0.000	0.000	0.000	0.000
20	A	19	ILE	0	0.118	0.022	30.218	-0.009	-0.009	0.000	0.000	0.000	0.000
21	A	20	VAL	0	0.006	0.014	29.334	-0.015	-0.015	0.000	0.000	0.000	0.000
22	A	21	ASP	-1	-0.838	-0.891	29.258	-0.202	-0.202	0.000	0.000	0.000	0.000
23	A	22	LEU	0	-0.012	-0.007	26.496	-0.015	-0.015	0.000	0.000	0.000	0.000
24	A	23	ALA	0	0.019	0.004	25.133	-0.025	-0.025	0.000	0.000	0.000	0.000
25	A	24	GLU	-1	-0.877	-0.917	24.260	-0.288	-0.288	0.000	0.000	0.000	0.000
26	A	25	ARG	1	0.797	0.877	24.350	0.193	0.193	0.000	0.000	0.000	0.000
27	A	26	ILE	0	0.075	0.018	20.057	-0.029	-0.029	0.000	0.000	0.000	0.000
28	A	27	SER	0	-0.086	-0.051	19.834	-0.050	-0.050	0.000	0.000	0.000	0.000
29	A	28	LYS	1	0.809	0.893	19.954	0.287	0.287	0.000	0.000	0.000	0.000
30	A	29	LEU	0	-0.027	0.002	17.214	-0.009	-0.009	0.000	0.000	0.000	0.000
31	A	30	ASP	-1	-0.889	-0.948	13.451	-0.775	-0.775	0.000	0.000	0.000	0.000
32	A	31	GLY	0	-0.032	-0.013	11.932	-0.080	-0.080	0.000	0.000	0.000	0.000
33	A	32	VAL	0	-0.050	-0.014	12.619	-0.061	-0.061	0.000	0.000	0.000	0.000
34	A	33	GLU	-1	-0.924	-0.961	11.934	-1.116	-1.116	0.000	0.000	0.000	0.000
35	A	34	GLY	0	-0.024	-0.014	16.518	0.079	0.079	0.000	0.000	0.000	0.000
36	A	35	VAL	0	-0.006	-0.003	18.846	-0.028	-0.028	0.000	0.000	0.000	0.000
37	A	36	ASN	0	-0.075	-0.034	21.566	0.040	0.040	0.000	0.000	0.000	0.000
38	A	37	ILE	0	0.026	0.020	24.375	-0.002	-0.002	0.000	0.000	0.000	0.000
39	A	38	SER	0	-0.021	-0.007	26.958	0.015	0.015	0.000	0.000	0.000	0.000
40	A	39	VAL	0	-0.023	-0.019	29.850	-0.002	-0.002	0.000	0.000	0.000	0.000
41	A	40	THR	0	-0.041	-0.027	30.387	0.000	0.000	0.000	0.000	0.000	0.000
42	A	41	ASP	-1	-0.915	-0.948	33.273	-0.104	-0.104	0.000	0.000	0.000	0.000
43	A	42	MET	0	-0.035	-0.026	35.931	-0.009	-0.009	0.000	0.000	0.000	0.000
44	A	43	ASP	-1	-0.842	-0.881	38.548	-0.087	-0.087	0.000	0.000	0.000	0.000
45	A	44	VAL	0	-0.044	-0.042	41.255	-0.001	-0.001	0.000	0.000	0.000	0.000
46	A	45	GLU	-1	-0.967	-0.990	40.805	-0.086	-0.086	0.000	0.000	0.000	0.000
47	A	46	THR	0	-0.024	-0.016	36.567	-0.004	-0.004	0.000	0.000	0.000	0.000
48	A	47	MET	0	-0.070	-0.042	34.026	0.001	0.001	0.000	0.000	0.000	0.000
49	A	48	GLY	0	0.069	0.041	32.672	-0.006	-0.006	0.000	0.000	0.000	0.000
50	A	49	LEU	0	-0.036	-0.030	28.840	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	50	MET	0	0.062	0.048	25.167	0.000	0.000	0.000	0.000	0.000	0.000
52	A	51	ILE	0	-0.037	-0.028	22.052	-0.007	-0.007	0.000	0.000	0.000	0.000
53	A	52	ILE	0	0.016	0.008	19.642	-0.012	-0.012	0.000	0.000	0.000	0.000
54	A	53	ILE	0	-0.006	-0.003	16.247	-0.001	-0.001	0.000	0.000	0.000	0.000
55	A	54	GLU	-1	-0.832	-0.918	14.919	-0.499	-0.499	0.000	0.000	0.000	0.000
56	A	55	GLY	0	0.049	0.018	12.799	0.057	0.057	0.000	0.000	0.000	0.000
57	A	56	THR	0	-0.091	-0.059	6.841	-0.289	-0.289	0.000	0.000	0.000	0.000
58	A	57	SER	0	-0.066	-0.039	6.163	-0.073	-0.073	0.000	0.000	0.000	0.000
59	A	58	LEU	0	0.004	0.025	8.022	0.254	0.254	0.000	0.000	0.000	0.000
60	A	59	ASN	0	-0.005	-0.019	11.298	0.008	0.008	0.000	0.000	0.000	0.000
61	A	60	PHE	0	0.025	0.001	13.249	0.090	0.090	0.000	0.000	0.000	0.000
62	A	61	ASP	-1	-0.858	-0.927	15.653	-0.281	-0.281	0.000	0.000	0.000	0.000
63	A	62	ASP	-1	-0.877	-0.925	16.761	-0.456	-0.456	0.000	0.000	0.000	0.000
64	A	63	ILE	0	0.003	0.005	15.979	0.043	0.043	0.000	0.000	0.000	0.000
65	A	64	ARG	1	0.872	0.928	19.480	0.249	0.249	0.000	0.000	0.000	0.000
66	A	65	LYS	1	0.858	0.924	19.819	0.368	0.368	0.000	0.000	0.000	0.000
67	A	66	MET	0	0.021	0.022	22.307	0.020	0.020	0.000	0.000	0.000	0.000
68	A	67	LEU	0	-0.014	-0.021	22.623	0.023	0.023	0.000	0.000	0.000	0.000
69	A	68	GLU	-1	-0.875	-0.923	25.481	-0.179	-0.179	0.000	0.000	0.000	0.000
70	A	69	GLU	-1	-0.962	-0.976	26.236	-0.230	-0.230	0.000	0.000	0.000	0.000
71	A	70	GLU	-1	-0.864	-0.890	27.744	-0.203	-0.203	0.000	0.000	0.000	0.000
72	A	71	GLY	0	-0.068	-0.034	30.092	0.009	0.009	0.000	0.000	0.000	0.000
73	A	72	CYS	0	-0.109	-0.055	27.820	0.009	0.009	0.000	0.000	0.000	0.000
74	A	73	ALA	0	0.028	0.015	28.488	-0.001	-0.001	0.000	0.000	0.000	0.000
75	A	74	ILE	0	-0.023	-0.017	22.050	-0.005	-0.005	0.000	0.000	0.000	0.000
76	A	75	HIS	0	-0.123	-0.061	26.344	0.019	0.019	0.000	0.000	0.000	0.000
77	A	76	SER	0	-0.007	-0.031	25.545	0.014	0.014	0.000	0.000	0.000	0.000
78	A	77	ILE	0	-0.049	-0.016	18.687	-0.022	-0.022	0.000	0.000	0.000	0.000
79	A	78	ASP	-1	-0.846	-0.897	21.983	-0.146	-0.146	0.000	0.000	0.000	0.000
80	A	79	GLU	-1	-0.914	-0.958	17.542	-0.226	-0.226	0.000	0.000	0.000	0.000
81	A	80	VAL	0	-0.027	-0.013	13.197	-0.045	-0.045	0.000	0.000	0.000	0.000
82	A	81	VAL	0	-0.001	0.018	11.474	0.055	0.055	0.000	0.000	0.000	0.000
83	A	82	SER	0	0.010	-0.004	8.156	-0.268	-0.268	0.000	0.000	0.000	0.000
84	A	83	GLY	0	0.005	0.005	5.319	0.366	0.366	0.000	0.000	0.000	0.000
85	A	84	ASN	0	-0.012	-0.029	3.635	-1.062	-0.773	0.009	-0.121	-0.176	-0.001
86	A	85	ARG	1	0.940	0.964	5.976	-0.260	-0.260	0.000	0.000	0.000	0.000
87	A	86	ILE	0	0.076	0.048	9.693	0.020	0.020	0.000	0.000	0.000	0.000
88	A	87	ILE	0	-0.101	-0.045	12.186	0.094	0.094	0.000	0.000	0.000	0.000
89	A	88	GLU	-1	-0.766	-0.852	14.639	-0.282	-0.282	0.000	0.000	0.000	0.000
90	A	89	GLY	0	-0.003	0.002	18.136	0.042	0.042	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:GLY)